8YAQ | pdb_00008yaq

Cryo-EM structure of cellodextrin phosphorylase from Clostridium thermocellum with cellodextrin ligands

• PDB DOI: https://doi.org/10.2210/pdb8YAQ/pdb
• EM Map EMD-39104: EMDB EMDataResource

• Classification: CARBOHYDRATE
• Organism(s): Acetivibrio thermocellus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-02-09 Released: 2025-02-12 
• Deposition Author(s): Kuga, T., Sunagawa, N., Igarashi, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Structure and dynamics of cellodextrin phosphorylase from Clostridium thermocellum determine chain length and crystalline packing of highly ordered cellulose II synthesized in vitro

Kuga, T., Sunagawa, N., Igarashi, K.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 226.71 kDa 
• Atom Count: 15,860 
• Modeled Residue Count: 1,969 
• Deposited Residue Count: 1,980 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellodextrin phosphorylase	A, B	990	Acetivibrio thermocellus	Mutation(s): 0  Gene Names: cdp-ym4
UniProt
Find proteins for Q93HT8 (Acetivibrio thermocellus) Explore Q93HT8  Go to UniProtKB:  Q93HT8

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	C [auth D]	5		N/A
Glycosylation Resources
GlyTouCan:  G91683DU GlyCosmos:  G91683DU

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	D [auth C]	3		N/A
Glycosylation Resources
GlyTouCan:  G14338VK GlyCosmos:  G14338VK GlyGen:  G14338VK

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth B], H [auth B], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 2 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900016	C [auth D]	beta-cellopentaose	Oligosaccharide / Metabolism

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900021	D [auth C]	beta-cellotriose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.4.0
MODEL REFINEMENT	PHENIX	1.20

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-12 
Deposition Author(s): Kuga, T., Sunagawa, N., Igarashi, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	22J12566
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	18H05494

Revision History  

• Version 1.0: 2025-02-12
  Type: Initial release